Membrane rafts represent small microdomains, evidenced most notably in the extracellular leaflet of the plasma membrane where they involve cholesterol, sphingolipids, and phospholipids with saturated acyl chains. A large number of biological functions have been identified to involve rafts, ranging from signal transduction and membrane traffic to viral coat assembly and toxin-induced pore formation. Seemingly unrelated diseases appear in the raft context: Alzheimer's disease, prion diseases, viral infections, and cholesterol biosynthesis disorders. In spite of accumulating needs to relate the raft concept to human diseases, even most basic aspects of membrane rafts are poorly understood; entirely unknown is how microdomain formation is coupled across the two membrane leaflets and, related, how protein-decorated lipid rafts convey information to the interior of the cell. A putative mechanism postulates structural coupling through conformational changes of trans-membrane proteins. We suggest an entirely different mechanism, namely a thermodynamic one, based on protein-induced lateral and trans-monolayer raft reorganization. That is, cooperative association of proteins with membrane rafts modifies the activity of cholesterol, leading besides lateral raft reorganization also to trans-monolayer coupling through cholesterol flip-flop. To test our hypothesis we construct a combined theoretical/experimental model system for protein-induced domain formation and cholesterol-mediated thermodynamic coupling of membrane domains across the bilayer. Specifically, we develop microscopic-level interaction models for cholesterol-containing membranes in the presence of associated proteins, we analyze the corresponding thermodynamic phase behavior, and we investigate the relation of thermodynamic and structural trans-monolayer coupling mechanisms. The modeling part employs microscopic-level and mean-field computational approaches such as Poisson- Boltzmann theory, chain packing theory, and membrane elasticity theory. In the experimental part, cholesterol activity will be deduced from binding isotherms of proteins onto mixed, cholesterol-containing membranes. Our proposed research is part of a new initiative in the Department of Physics at North Dakota State University to establish a focus in soft condensed matter and biophysical applications, and to expose graduate/undergraduate students to interdisciplinary research involving computational methods. [unreadable] [unreadable] [unreadable] [unreadable]